Quantitative structure-activity relationship (QSAR) is the mathematical relationship between biological activity and molecular structure. QSAR analyses were carried out for series of 45 Naphthylisoquinoline and 22 Bisbenzylisoquinoline alkaloids to find out the structural features (molecular descriptors) responsible for their antimalarial activities as well as the cytotoxicity. The 3D structures of all the structures were fully optimised in Spartan 14 v.1.1.0 using density functional B3LYP and the standard Pople¿s basis set of 6-311G*. The combination of the Genetic algorithm (GA) and Multiple Linear Regression (MLR) analyses methods applied lead to QSAR models from the descriptors that can be used to predict activities and cytotoxicity of new alkaloids.